There is no tree in this file.

[jiq7885]

1st issues with no responce show in newick file .

Alignment: roaryressult/core_gene_alignment.aln
Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
TopHits: 1.00*sqrtN close=default refresh=0.80
ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
Initial topology in 1.29 seconds
Refining topology: 10 rounds ME-NNIs, 2 rounds ME-SPRs, 5 rounds ML-NNIs
Total branch-length 0.013 after 10.20 sec 1 of 4 splits
ML-NNI round 1: LogLk = -3018137.577 NNIs 0 max delta 0.00 Time 28.09
GTR Frequencies: 0.3563 0.1470 0.1906 0.3061ep 12 of 12
GTR rates(ac ag at cg ct gt) 1.3849 4.0239 1.3679 0.9235 6.3455 1.0000
Switched to using 20 rate categories (CAT approximation)20 of 20
Rate categories were divided by 0.626 so that average rate = 1.0
CAT-based log-likelihoods may not be comparable across runs
Use -gamma for approximate but comparable Gamma(20) log-likelihoods
ML-NNI round 2: LogLk = -2882836.960 NNIs 0 max delta 0.00 Time 161.39
Turning off heuristics for final round of ML NNIs (converged)
ML-NNI round 3: LogLk = -2882836.948 NNIs 0 max delta 0.00 Time 188.80 (final)
Optimize all lengths: LogLk = -2882836.948 Time 198.09

Killed

2nd issues with no trees option in file to build tree by script.

File "roary_plots.py", line 77, in
t = Phylo.read(options.tree, 'newick')
File "/home/j/miniconda3/envs/pangenome/lib/python3.7/site-packages/Bio/Phylo/_io.py", line 62, in read
raise ValueError("There are no trees in this file.") from None
ValueError: There are no trees in this file.

so, anyone please help to solve this two problems.